Load Data from the Clock Calculator

Table with summarize info [table 1]

For all observations (including the control group)

Characteristic N = 1411
Group
LCW Clean Ctrl 12 / 141 (8.5%)
LEX 129 / 141 (91%)
Gender
F 140 / 141 (99%)
U 1 / 141 (0.7%)
DNAmAge 57 (14)
DNAmAgeHannum 60 (14)
DNAmPhenoAge 56 (13)
DNAmAgeSkinBloodClock 56 (13)
DNAmGrimAge 56 (11)
DNAmTL 6.80 (0.33)
AgeAccelerationResidual -0.1 (5.1)
AgeAccelerationResidualHannum -0.1 (4.9)
AgeAccelPheno -0.1 (5.1)
DNAmAgeSkinBloodClockAdjAge 0.0 (3.7)
AgeAccelGrim -0.1 (3.4)
DNAmTLAdjAge 0.00 (0.24)
IEAA 0.0 (4.5)
EEAA -0.1 (6.0)
Age 57 (14)
county
Fuyuan 61 / 119 (51%)
Xuanwe 58 / 119 (49%)
(Missing) 22
BMI 22.0 (3.5)
(Missing) 12
ses 54 / 119 (45%)
(Missing) 22
edu
1 81 / 119 (68%)
2 19 / 119 (16%)
3 14 / 119 (12%)
4 5 / 119 (4.2%)
(Missing) 22
curFuel
Gas/Elect 12 / 124 (9.7%)
Smokeles 17 / 124 (14%)
Smoky 87 / 124 (70%)
Wood_and_or_Plant 8 / 124 (6.5%)
(Missing) 17
brthFuel
Gas/Elect 12 / 128 (9.4%)
Mix 53 / 128 (41%)
Smokeles 5 / 128 (3.9%)
Smoky 47 / 128 (37%)
Wood 11 / 128 (8.6%)
(Missing) 13
cumFuel
Gas/Elect 12 / 131 (9.2%)
Mix 82 / 131 (63%)
Smoky 37 / 131 (28%)
(Missing) 10
curStove
Firepit_and_unventilated 22 / 124 (18%)
Gas/Elect 12 / 124 (9.7%)
Mix 19 / 124 (15%)
Portable_stove 20 / 124 (16%)
Ventilated 51 / 124 (41%)
(Missing) 17
bap_air 65 (87)
(Missing) 17
pm25_air 197 (176)
(Missing) 12
ANY_air 1,038 (1,792)
(Missing) 53
BPE_air 71 (92)
(Missing) 17
BaA_air 88 (145)
(Missing) 17
BbF_air 106 (143)
(Missing) 17
BkF_air 23 (32)
(Missing) 17
CHR_air 83 (133)
(Missing) 17
DBA_air 24 (36)
(Missing) 17
FLT_air 60 (136)
(Missing) 17
FLU_air 486 (680)
(Missing) 53
IPY_air 43 (51)
(Missing) 17
NAP_air 5,731 (8,737)
(Missing) 53
PHE_air 730 (1,054)
(Missing) 53
PYR_air 66 (139)
(Missing) 17
Benzanthracene_Chrysene_urine 0.92 (3.17)
(Missing) 14
Naphthalene_urine 224 (686)
(Missing) 12
Methylnaphthalene_2_urine 46 (59)
(Missing) 21
Methylnaphthalene_1_urine 20 (24)
(Missing) 16
Acenaphthene_urine 7 (11)
(Missing) 12
Phenanthrene_Anthracene_urine 204 (275)
(Missing) 12
Fluoranthene_urine 21 (23)
(Missing) 12
Pyrene_urine 0.71 (0.57)
(Missing) 30
CUR6_BC_PAH6 0.21 (0.98)
(Missing) 25
CUR6_PAH31 0.20 (0.92)
(Missing) 25
CUR6_NkF -0.11 (1.10)
(Missing) 25
CUR6_PM_RET -0.01 (0.93)
(Missing) 25
CUR6_NO2 0.19 (0.99)
(Missing) 25
CUR6_SO2 -0.13 (0.89)
(Missing) 25
CHLD5_X7 -0.02 (0.92)
(Missing) 25
CHLD5_X33 0.18 (0.98)
(Missing) 25
CHLD5_NkF -0.11 (1.13)
(Missing) 25
CHLD5_NO2 0.23 (1.09)
(Missing) 25
CHLD5_SO2 0.02 (0.88)
(Missing) 25
CUM6_BC_NO2_PM 0.11 (1.01)
(Missing) 25
CUM6_PAH36 0.21 (0.97)
(Missing) 25
CUM6_DlP -0.20 (1.04)
(Missing) 25
CUM6_NkF -0.04 (1.11)
(Missing) 25
CUM6_RET -0.09 (0.97)
(Missing) 25
CUM6_SO2 -0.07 (0.93)
(Missing) 25
MEAS6_BC_PM_RET 0.04 (0.93)
(Missing) 97
MEAS6_X31 0.06 (1.05)
(Missing) 97
MEAS6_X5 0.01 (1.00)
(Missing) 97
MEAS6_DlP 0.02 (1.00)
(Missing) 97
MEAS6_NkF 0.08 (1.04)
(Missing) 97
MEAS6_NO2_SO2 -0.03 (0.99)
(Missing) 97
URI5_NAP_1M_2M 0.01 (0.96)
(Missing) 37
URI5_ACE -0.06 (0.99)
(Missing) 37
URI5_FLU_PHE -0.05 (0.95)
(Missing) 37
URI5_PYR -0.02 (0.91)
(Missing) 37
URI5_CHR -0.01 (1.01)
(Missing) 37

1 n / N (%); Mean (SD)

For observations in the treatment group

Characteristic N = 1291
SbjctD 297 (129)
(Missing) 10
Visit
1 91 / 119 (76%)
2 28 / 119 (24%)
(Missing) 10
Group
LEX 129 / 129 (100%)
Gender
F 128 / 129 (99%)
U 1 / 129 (0.8%)
DNAmAge 58 (13)
DNAmAgeHannum 60 (14)
DNAmPhenoAge 56 (14)
DNAmAgeSkinBloodClock 57 (13)
DNAmGrimAge 56 (11)
DNAmTL 6.82 (0.32)
AgeAccelerationResidual 0.4 (4.7)
AgeAccelerationResidualHannum -0.2 (4.0)
AgeAccelPheno -0.3 (4.3)
DNAmAgeSkinBloodClockAdjAge 0.2 (3.4)
AgeAccelGrim -0.43 (2.99)
DNAmTLAdjAge 0.03 (0.18)
IEAA 0.2 (4.3)
EEAA -0.3 (5.1)
Age 58 (15)
county
Fuyuan 61 / 119 (51%)
Xuanwe 58 / 119 (49%)
(Missing) 10
BMI 22.0 (3.5)
ses 54 / 119 (45%)
(Missing) 10
edu
1 81 / 119 (68%)
2 19 / 119 (16%)
3 14 / 119 (12%)
4 5 / 119 (4.2%)
(Missing) 10
curFuel
Smokeles 17 / 112 (15%)
Smoky 87 / 112 (78%)
Wood_and_or_Plant 8 / 112 (7.1%)
(Missing) 17
brthFuel
Mix 53 / 116 (46%)
Smokeles 5 / 116 (4.3%)
Smoky 47 / 116 (41%)
Wood 11 / 116 (9.5%)
(Missing) 13
cumFuel
Mix 82 / 119 (69%)
Smoky 37 / 119 (31%)
(Missing) 10
curStove
Firepit_and_unventilated 22 / 112 (20%)
Mix 19 / 112 (17%)
Portable_stove 20 / 112 (18%)
Ventilated 51 / 112 (46%)
(Missing) 17
bap_air 65 (87)
(Missing) 5
pm25_air 197 (176)
ANY_air 1,038 (1,792)
(Missing) 41
BPE_air 71 (92)
(Missing) 5
BaA_air 88 (145)
(Missing) 5
BbF_air 106 (143)
(Missing) 5
BkF_air 23 (32)
(Missing) 5
CHR_air 83 (133)
(Missing) 5
DBA_air 24 (36)
(Missing) 5
FLT_air 60 (136)
(Missing) 5
FLU_air 486 (680)
(Missing) 41
IPY_air 43 (51)
(Missing) 5
NAP_air 5,731 (8,737)
(Missing) 41
PHE_air 730 (1,054)
(Missing) 41
PYR_air 66 (139)
(Missing) 5
Benzanthracene_Chrysene_urine 0.92 (3.17)
(Missing) 2
Naphthalene_urine 224 (686)
Methylnaphthalene_2_urine 46 (59)
(Missing) 9
Methylnaphthalene_1_urine 20 (24)
(Missing) 4
Acenaphthene_urine 7 (11)
Phenanthrene_Anthracene_urine 204 (275)
Fluoranthene_urine 21 (23)
Pyrene_urine 0.71 (0.57)
(Missing) 18
CUR6_BC_PAH6 0.21 (0.98)
(Missing) 13
CUR6_PAH31 0.20 (0.92)
(Missing) 13
CUR6_NkF -0.11 (1.10)
(Missing) 13
CUR6_PM_RET -0.01 (0.93)
(Missing) 13
CUR6_NO2 0.19 (0.99)
(Missing) 13
CUR6_SO2 -0.13 (0.89)
(Missing) 13
CHLD5_X7 -0.02 (0.92)
(Missing) 13
CHLD5_X33 0.18 (0.98)
(Missing) 13
CHLD5_NkF -0.11 (1.13)
(Missing) 13
CHLD5_NO2 0.23 (1.09)
(Missing) 13
CHLD5_SO2 0.02 (0.88)
(Missing) 13
CUM6_BC_NO2_PM 0.11 (1.01)
(Missing) 13
CUM6_PAH36 0.21 (0.97)
(Missing) 13
CUM6_DlP -0.20 (1.04)
(Missing) 13
CUM6_NkF -0.04 (1.11)
(Missing) 13
CUM6_RET -0.09 (0.97)
(Missing) 13
CUM6_SO2 -0.07 (0.93)
(Missing) 13
MEAS6_BC_PM_RET 0.04 (0.93)
(Missing) 85
MEAS6_X31 0.06 (1.05)
(Missing) 85
MEAS6_X5 0.01 (1.00)
(Missing) 85
MEAS6_DlP 0.02 (1.00)
(Missing) 85
MEAS6_NkF 0.08 (1.04)
(Missing) 85
MEAS6_NO2_SO2 -0.03 (0.99)
(Missing) 85
URI5_NAP_1M_2M 0.01 (0.96)
(Missing) 25
URI5_ACE -0.06 (0.99)
(Missing) 25
URI5_FLU_PHE -0.05 (0.95)
(Missing) 25
URI5_PYR -0.02 (0.91)
(Missing) 25
URI5_CHR -0.01 (1.01)
(Missing) 25

1 Mean (SD); n / N (%)

For observations in the control group

Characteristic N = 121
SbjctD NA (NA)
(Missing) 12
Visit NA (NA)
(Missing) 12
Group
LCW Clean Ctrl 12 / 12 (100%)
Gender
F 12 / 12 (100%)
DNAmAge 46 (14)
DNAmAgeHannum 55 (10)
DNAmPhenoAge 53 (10)
DNAmAgeSkinBloodClock 48 (12)
DNAmGrimAge 54 (8)
DNAmTL 6.66 (0.44)
AgeAccelerationResidual -5 (7)
AgeAccelerationResidualHannum 2 (10)
AgeAccelPheno 3 (10)
DNAmAgeSkinBloodClockAdjAge -2.1 (5.9)
AgeAccelGrim 3.6 (5.4)
DNAmTLAdjAge -0.26 (0.51)
IEAA -2.6 (6.1)
EEAA 2 (12)
Age 50 (11)
county 0 / 0 (NA%)
(Missing) 12
BMI NA (NA)
(Missing) 12
ses NA (NA)
(Missing) 12
edu NA (NA)
(Missing) 12
curFuel
Gas/Elect 12 / 12 (100%)
brthFuel
Gas/Elect 12 / 12 (100%)
cumFuel
Gas/Elect 12 / 12 (100%)
curStove
Gas/Elect 12 / 12 (100%)
bap_air NA (NA)
(Missing) 12
pm25_air NA (NA)
(Missing) 12
ANY_air NA (NA)
(Missing) 12
BPE_air NA (NA)
(Missing) 12
BaA_air NA (NA)
(Missing) 12
BbF_air NA (NA)
(Missing) 12
BkF_air NA (NA)
(Missing) 12
CHR_air NA (NA)
(Missing) 12
DBA_air NA (NA)
(Missing) 12
FLT_air NA (NA)
(Missing) 12
FLU_air NA (NA)
(Missing) 12
IPY_air NA (NA)
(Missing) 12
NAP_air NA (NA)
(Missing) 12
PHE_air NA (NA)
(Missing) 12
PYR_air NA (NA)
(Missing) 12
Benzanthracene_Chrysene_urine NA (NA)
(Missing) 12
Naphthalene_urine NA (NA)
(Missing) 12
Methylnaphthalene_2_urine NA (NA)
(Missing) 12
Methylnaphthalene_1_urine NA (NA)
(Missing) 12
Acenaphthene_urine NA (NA)
(Missing) 12
Phenanthrene_Anthracene_urine NA (NA)
(Missing) 12
Fluoranthene_urine NA (NA)
(Missing) 12
Pyrene_urine NA (NA)
(Missing) 12
CUR6_BC_PAH6 NA (NA)
(Missing) 12
CUR6_PAH31 NA (NA)
(Missing) 12
CUR6_NkF NA (NA)
(Missing) 12
CUR6_PM_RET NA (NA)
(Missing) 12
CUR6_NO2 NA (NA)
(Missing) 12
CUR6_SO2 NA (NA)
(Missing) 12
CHLD5_X7 NA (NA)
(Missing) 12
CHLD5_X33 NA (NA)
(Missing) 12
CHLD5_NkF NA (NA)
(Missing) 12
CHLD5_NO2 NA (NA)
(Missing) 12
CHLD5_SO2 NA (NA)
(Missing) 12
CUM6_BC_NO2_PM NA (NA)
(Missing) 12
CUM6_PAH36 NA (NA)
(Missing) 12
CUM6_DlP NA (NA)
(Missing) 12
CUM6_NkF NA (NA)
(Missing) 12
CUM6_RET NA (NA)
(Missing) 12
CUM6_SO2 NA (NA)
(Missing) 12
MEAS6_BC_PM_RET NA (NA)
(Missing) 12
MEAS6_X31 NA (NA)
(Missing) 12
MEAS6_X5 NA (NA)
(Missing) 12
MEAS6_DlP NA (NA)
(Missing) 12
MEAS6_NkF NA (NA)
(Missing) 12
MEAS6_NO2_SO2 NA (NA)
(Missing) 12
URI5_NAP_1M_2M NA (NA)
(Missing) 12
URI5_ACE NA (NA)
(Missing) 12
URI5_FLU_PHE NA (NA)
(Missing) 12
URI5_PYR NA (NA)
(Missing) 12
URI5_CHR NA (NA)
(Missing) 12

1 Mean (SD); n / N (%)

Fuel Types Summary table

Current Fuel vs Birth Fuel + Cumulative

##    brthFuel   cumFuel Gas/Elect Smokeles Smoky Wood_and_or_Plant NA
## 1 Gas/Elect Gas/Elect        12        0     0                 0  0
## 2       Mix       Mix         0        9    36                 6  2
## 3  Smokeles       Mix         0        2     3                 0  0
## 4     Smoky       Mix         0        3     7                 0  0
## 5     Smoky     Smoky         0        0    35                 0  2
## 6      Wood       Mix         0        2     4                 2  3
## 7      <NA>       Mix         0        1     2                 0  0
## 8      <NA>      <NA>         0        0     0                 0 10

PCA

Only the treatment group are used in this PCA exploration.

Explore clocks

Clock values

Correlogram

Between clocks

{r correlation_clocks, fig.height=6, fig.width=6} # library(corrplot) # corrplot(cor(df[,c("Age", clocks_vars)]), addCoef.col = 'black', type = 'lower') #

All subjects

Control Group

Treatment Group

Median absolute error

##               DNAmAge         DNAmAgeHannum          DNAmPhenoAge 
##              3.645646              3.595255              3.061584 
## DNAmAgeSkinBloodClock           DNAmGrimAge 
##              2.585191              3.993800

Scatterplots of age vs each epigenetic age

All subjects

Control Group

Treatment Group

Explore Exposure Measurements

Correlogram

Between Ambient Exposure Measurements

Between Urinary Exposure Measurements

Between Ambient and Urinary Exposure Measurements

Clocks vs Measurements

Pairplots